README.md

amber_meta

This repository integrates a few routines to launch amber in a systematic manner.

Getting the code

git clone https://github.com/macrocosme/amber_meta.git
cd amber_meta/

Usage

The most basic usage is via python amber_run.py, and parameters that will be prompted.

Else, more advanced usage involves functions not yet added to amber_runs's main. In an ipython session:

import amber_meta.amber_run as ar
import amber_meta.amber_plot as ap

# Run amber using root scenario yaml file
'''
The amber job(s) will run independently. The following steps currently
involves that these jobs have terminated and their .trigger outputs
be available.
'''
imput_file = 'yaml/root/root.yaml'
ar.run_amber_from_yaml_root(
  input_file,
  root='subband',
  verbose=False,
  print_only=True
) # Print only will not launch the amber job. When False, the command will be run via subprocess.

# Read amber output .trigger files (e.g. steps 1..N) pooled into a pandas dataframe
df = ar.get_amber_run_results_from_root_yaml(
  input_file,
  root='subband',
  verbose=False
)

# Make pair plot from output
pairplot(
  df,
  output_name='../pairplot.pdf'
)

Example of root yaml file

# AMBER setup for bruteforce dedispersion
bruteforce:
    input_file: 'path/to/filterbank.fil'
    n_cpu: 1
    base_name: 'scenario_base_name'
    base_scenario_path: 'scenario/' # Path where amber scenario files live
    scenario_files:  ['tuning.sh']
    snrmin: 8
    base_config_path: 'configuration/' # Path where amber configuration files live
    config_repositories: ['scenario_base_name']
    debug: False
    rfim: True
    rfim_mode: 'time_domain_sigma_cut'
    rfim_threshold: None
    snr_mode: 'snr_mom_sigmacut'
    input_data_mode: 'sigproc'
    output_dir: 'results/'
    verbose: True
    print_only: False
# AMBER setup for subband dedispersion
subband:
    input_file: 'path/to/filterbank.fil'
    n_cpu: 3
    base_name: 'scenario_base_name'
    base_scenario_path: 'scenario/'
    scenario_files:  [
        'tuning_1.sh',
        'tuning_2.sh',
        'tuning_3.sh'
      ]
    snrmin: 8
    base_config_path: 'configuration/'
    config_repositories: [
        'scenario_base_name_step1',
        'scenario_base_name_step2',
        'scenario_base_name_step3'
      ]
    debug: False
    rfim: True
    rfim_mode: 'time_domain_sigma_cut'
    rfim_threshold: None
    snr_mode: 'snr_mom_sigmacut'
    input_data_mode: 'sigproc'
    output_dir: 'results/'
    verbose: True
    print_only: False

Issues

If you have any issues with this code, please file an issue on github. Please note that the development branch may be ahead of the master branch, as I am currently a one-man band.

License

This project is Copyright (c) D. Vohl and licensed under the terms of the GNU GPL v3+ license.